6Y88

IGPS (Indole-3-glycerol phosphate synthase) from Pseudomonas aeruginosa in complex with substrate inhibitor rCdRP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structure and kinetics of indole-3-glycerol phosphate synthase from Pseudomonas aeruginosa : Decarboxylation is not essential for indole formation.

Soderholm, A.Newton, M.S.Patrick, W.M.Selmer, M.

(2020) J Biol Chem 295: 15948-15956

  • DOI: https://doi.org/10.1074/jbc.RA120.014936
  • Primary Citation of Related Structures:  
    6Y88

  • PubMed Abstract: 

    In tryptophan biosynthesis, the reaction catalyzed by the enzyme indole-3-glycerol phosphate synthase (IGPS) starts with a condensation step in which the substrate's carboxylated phenyl group makes a nucleophilic attack to form the pyrrole ring of the indole, followed by a decarboxylation that restores the aromaticity of the phenyl. IGPS from Pseudomonas aeruginosa has the highest turnover number of all characterized IGPS enzymes, providing an excellent model system to test the necessity of the decarboxylation step. Since the 1960s, this step has been considered to be mechanistically essential based on studies of the IGPS-phosphoribosylanthranilate isomerase fusion protein from Escherichia coli Here, we present the crystal structure of P. aeruginosa IGPS in complex with reduced CdRP, a nonreactive substrate analog, and using a sensitive discontinuous assay, we demonstrate weak promiscuous activity on the decarboxylated substrate 1-(phenylamino)-1-deoxyribulose-5-phosphate, with an ∼1000× lower rate of IGP formation than from the native substrate. We also show that E. coli IGPS, at an even lower rate, can produce IGP from decarboxylated substrate. Our structure of P. aeruginosa IGPS has eight molecules in the asymmetric unit, of which seven contain ligand and one displays a previously unobserved conformation closer to the reactive state. One of the few nonconserved active-site residues, Phe 201 in P. aeruginosa IGPS, is by mutagenesis demonstrated to be important for the higher turnover of this enzyme on both substrates. Our results demonstrate that despite IGPS's classification as a carboxy-lyase ( i.e. decarboxylase), decarboxylation is not a completely essential step in its catalysis.


  • Organizational Affiliation

    Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden. Electronic address: annika.soderholm@kemi.uu.se.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Indole-3-glycerol phosphate synthase
A, B, C, D, E
A, B, C, D, E, F, H
287Pseudomonas aeruginosaMutation(s): 0 
Gene Names: trpCDT376_13060
EC: 4.1.1.48
UniProt
Find proteins for P20577 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore P20577 
Go to UniProtKB:  P20577
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20577
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Indole-3-glycerol phosphate synthase,Indole-3-glycerol phosphate synthase277Pseudomonas aeruginosaMutation(s): 0 
Gene Names: trpCDT376_13060
EC: 4.1.1.48
UniProt
Find proteins for P20577 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore P20577 
Go to UniProtKB:  P20577
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20577
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
137 (Subject of Investigation/LOI)
Query on 137

Download Ideal Coordinates CCD File 
I [auth A]
K [auth B]
N [auth C]
Q [auth D]
R [auth E]
I [auth A],
K [auth B],
N [auth C],
Q [auth D],
R [auth E],
U [auth F],
W [auth H]
1-(O-CARBOXY-PHENYLAMINO)-1-DEOXY-D-RIBULOSE-5-PHOSPHATE
C12 H18 N O9 P
AULMJMUNCOBRHC-MXWKQRLJSA-N
CIT
Query on CIT

Download Ideal Coordinates CCD File 
S [auth E]CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
V [auth G]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL
Query on GOL

Download Ideal Coordinates CCD File 
J [auth A]
L [auth B]
M [auth B]
O [auth C]
P [auth C]
J [auth A],
L [auth B],
M [auth B],
O [auth C],
P [auth C],
T [auth E],
X [auth H]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 164.705α = 90
b = 150.683β = 90
c = 114.38γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden2017-03827
Knut and Alice Wallenberg FoundationSwedenEvolution of new genes and proteins

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-23
    Type: Initial release
  • Version 1.1: 2020-09-30
    Changes: Database references
  • Version 1.2: 2020-12-02
    Changes: Database references
  • Version 1.3: 2024-01-24
    Changes: Data collection, Database references, Refinement description